Last Thursday I had a small adventure, the kind of thrill a big city can often throw up, if only you put in a little forward planning. It wasn't a promising morning: a soft rain was falling, and the sky was old-knicker grey. Nor was my destination exotic: Kilburn High Road, a relentless drag of kebab shops and charity shops. When I arrived at the precise spot, a dilapidated construction known as the Tin Tabernacle, I could find no way inside. But then… salvation! Someone showed me a bell, high above my head, and soon after ringing it, I walked into one of the most marvellous spaces I've seen in a long time. For me, this was love at first sight.

The Tin Tabernacle was built in 1863 by a developer called James Bailey. I say "built", but this is pushing it, really. Unlike Bailey's other projects – he specialised in the terraced houses you can still see in this part of north-west London today – this one came straight from the pages of a catalogue. Made of corrugated iron, it was a flat-pack church of the same ilk as the sweaty "God boxes" that were delivered to distant outposts of the Empire. It cost less than £1,000 and was intended only to be temporary. In the fullness of time, or so Bailey believed, the local Congregationalists would raise enough money to build a chapel all of their own.

In the end, though, this never happened, and the tabernacle lived on. In 1947 it was taken over by the Willesden & St Marylebone Sea Cadets, the charity that remains its custodian; the building is now grade II listed. This applies only to the exterior, which is a pity, for it's the interior that makes the eyes pop. In the 1950s the inside of the tabernacle was transformed by a group of local men so as to resemble the inside of a Royal Navy ship. There are portholes and rigging, a boatswain's store and a wardroom, and a proper bridge, complete with wheel and a full set of engine order telegraphs. Also, smack in the middle of the main deck, is a 1943 anti-aircraft gun.

Not that I knew any of this at first. For the next few weeks the Tin Tabernacle is home to an installation by the artist Lindsay Seers (a commission by Artangel, the remarkable charity which seeks to take art out of the gallery and into the world), and it's part of her design that visitors find out the peculiar nature of the building little by little. In the beginning I saw only the wardroom, with its tiny bar and a sign that urges officers to check they are correctly dressed. This is where you wait before the show begins, and it's adorable.

Seers works in film, constructing complex narratives that are mostly fiction but which have their roots in autobiography. When she started talking to the people at Artangel they took her to the tabernacle on a kind of blind date, and I'm guessing that, like me, she fell hard in love. For her, though, the building has an extra resonance. Seers's great great uncle, George Edwards, who was born in 1866, was a sea cadet who joined the merchant navy and sailed to Zanzibar, where he was involved in British efforts to dismantle the local slave trade. Look at the walls of the tabernacle's wardroom and it's possible you will find a photograph of George. You can't miss him. He has a distinctive appearance. His eyes were different colours.

Seers's film, Nowhere Less Now, is shown on two screens, one flat and round, the other spherical. In the flickering gloom you think, of course, of lenses, of George's eyes. But these screens also put you in mind of human eggs (his condition, heterochromia, was genetic), and of portholes. The narrative is multilayered, and stable as quicksand. It looks back to George's life onboard HMS Dragon, but also forward to a future in which photographs have been banned (those lucky enough to be in possession of a photograph must gaze on it in secret, gathering with others in a temporary structure not unlike the tabernacle). Seers also travels to Zanzibar, where George eventually drowned, and to Dar es Salaam, where she finds another church of corrugated iron. Unanswered questions hang heavy in the air. What compelled George's wife, Georgina, to wear a dress of such strange, Masonic design? (Seers films herself in something similar, with macabre results.) What happened to Seers's stepsister, who went missing as a child? And was it her uncle who carved his name on a huge baobab tree on Cemetery Island, or some other sailor called George?

After 20 minutes the film ends. Too soon. As the lights come up, you're still puzzling things out (a feeling that will last for days, and probably for ever). It takes a moment, then, to notice what the dark previously concealed: that Seers has made her own additions to the folk-art interior of the tabernacle, and that you're sitting in what appears to be the upturned hull of a ship. Knock its sides with a knuckle and you will hear the stark clank of metal. The disorientation doesn't end here. Afterwards, free to explore, I wandered into a tiny side chapel. It has a medieval altar and a lectern whose base is – wait for it – a cloven hoof. The effect was uncanny. Outside, the traffic rumbled; Kilburn could not be more landlocked if it tried. But in the strange quiet of the Tin Tabernacle I was lost at sea, overwhelmed by a briny wave of doubt and confusion.